trans.main
Class OverlapCounter

java.lang.Object
  trans.main.OverlapCounter

public class OverlapCounter

extends java.lang.Object

Provides an intersection analysis on multiple Interval[]s.

Constructor Summary

OverlapCounter(java.lang.String[] args)

Method Summary

void	findClosestPeaks(Interval[] one, Interval[] two, java.io.File fileOne, java.io.File fileTwo)
static int	findPeak(Interval i) Returns base position of highest scoring peak, if no peak uses middle of sub window if no sub window uses middle of interval
static void	main(java.lang.String[] args)
boolean	overlap(Interval one, Interval two) checks to see if intervals overlap by the minimum maxGap, can set maxGap negative to require an overlap.
int	overlapPeaks(Interval one, Interval two) Returns distance between top peaks.
static java.lang.String	percent(int overlaps, int total)
static void	printDocs()
static void	printTable(java.lang.Object[][] t, java.lang.String[] names)
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
static Interval[]	subtractIntervals(Interval[] bigger, Interval[] smaller) Returns the difference between two interval arrays, be sure to get bigger and smaller correct.
java.lang.String	testOverlap(Interval[] one, Interval[] two, java.io.File fileOne, java.io.File fileTwo) Returns the average % intersection.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OverlapCounter

public OverlapCounter(java.lang.String[] args)

Method Detail

printTable

public static void printTable(java.lang.Object[][] t,
                              java.lang.String[] names)

findClosestPeaks

public void findClosestPeaks(Interval[] one,
                             Interval[] two,
                             java.io.File fileOne,
                             java.io.File fileTwo)

overlapPeaks

public int overlapPeaks(Interval one,
                        Interval two)

Returns distance between top peaks. if no peak uses middle of sub window if no sub window uses middle of interval returns -1 if different chromosomes, 0 if direct match, 1 if immediately adjacent, 2 if 1bp gap...

findPeak

public static int findPeak(Interval i)

Returns base position of highest scoring peak, if no peak uses middle of sub window if no sub window uses middle of interval

overlap

public boolean overlap(Interval one,
                       Interval two)

checks to see if intervals overlap by the minimum maxGap, can set maxGap negative to require an overlap.

testOverlap

public java.lang.String testOverlap(Interval[] one,
                                    Interval[] two,
                                    java.io.File fileOne,
                                    java.io.File fileTwo)

Returns the average % intersection.

percent

public static java.lang.String percent(int overlaps,
                                       int total)

subtractIntervals

public static Interval[] subtractIntervals(Interval[] bigger,
                                           Interval[] smaller)

Returns the difference between two interval arrays, be sure to get bigger and smaller correct.

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()

main

public static void main(java.lang.String[] args)